Features to 3D from 2D in QGIS
You can use the v.to.3d module in the GRASS toolkit (installed with QGIS) to do 2d to 3d layer transformation:
v.to.3d - Performs transformation of 2D vector features to 3D.
I am using the QGIS 2.14 in portuguese, but I'll try to show you the steps with pics bellow.
1- Click in save as
2- On the "save window" choose the option "inclui dimensao-z" in english is equal to "include Z data" I think.